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Preliminary Study of Whole-Genome Bisulfite Sequencing and Transcriptome Sequencing in VHL Disease-Associated ccRCC

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Abstract

Background

Von Hippel–Lindau (VHL) disease is an autosomal dominant hereditary tumor syndrome with an incidence of approximately 1/36,000. VHL disease-associated clear cell renal cell carcinoma (ccRCC) is the most common congenital RCC. Although recent advances in treating RCC have improved the long-term prognosis of patients with VHL disease, kidney cancer is still the leading cause of death in these patients. Therefore, finding new targets for diagnosing and treating VHL disease-associated ccRCC is still essential.

Methods

In this study, we collected matched tumor tissues and normal samples from 25 patients with VHL disease-associated ccRCC, diagnosed and surgically treated in the Department of Urology, Peking University First Hospital. After screening, we performed whole genome bisulfite sequencing (WGBS) on 23 pairs of tissues and RNA-seq on 6 pairs of tissues. And we also compared the VHL disease-associated ccRCC transcriptome data with the sporadic ccRCC transcriptome data from the The Cancer Genome Atlas (TCGA) public database

Results

We found that the methylation level of VHL disease-associated ccRCC tumor tissues was significantly lower than that of normal tissues. The tumor tissues showed a difference in the copy number of 3p loss and 5q and 7q gain compared with normal tissues. We integrated RNA-seq and WGBS data to reveal methylation candidate genes associated with VHL disease-associated ccRCC; our results showed 124 hypermethylated and downregulated genes, and 245 hypomethylated and upregulated genes. By comparing the VHL disease-associated ccRCC transcriptome data with the sporadic ccRCC transcriptome data from the TCGA public database, we found that the major pathways of differential gene enrichment differed between them.

Conclusions

Our study mapped the multiomics of copy number variation, methylation and mRNA level changes in tumor and normal tissues of clear cell renal cell carcinoma with VHL syndrome, which provides a solid foundation for the mechanistic study, biomarker screening, and therapeutic target discovery of clear cell renal cell carcinoma.

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Acknowledgements

The authors thank Novogene Co. Ltd. for the sequencing service and The Cancer Genome Atlas for providing high-quality data.

Author information

Author notes

  1. Lei Li and Hainan Bao contributed equally to this work.

Authors and Affiliations

  1. Department of Urology, Peking University First Hospital, Beijing, 100034, China

    Lei Li, Yawei Xu, Wuping Yang, Zedan Zhang, Kenan Zhang, Jingcheng Zhou, Yanqing Gong & Kan Gong

  2. Institution of Urology, Peking University, Beijing, 100034, China

    Lei Li, Yawei Xu, Wuping Yang, Zedan Zhang, Kenan Zhang, Jingcheng Zhou, Yanqing Gong & Kan Gong

  3. Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China

    Lei Li, Yawei Xu, Wuping Yang, Zedan Zhang, Kenan Zhang, Jingcheng Zhou, Yanqing Gong & Kan Gong

  4. National Urological Cancer Center, Beijing, 100034, China

    Lei Li, Yawei Xu, Wuping Yang, Zedan Zhang, Kenan Zhang, Jingcheng Zhou, Yanqing Gong & Kan Gong

  5. Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China

    Hainan Bao & Weimin Ci

  6. University of Chinese Academy of Sciences, Beijing, 100049, China

    Hainan Bao & Weimin Ci

  7. Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China

    Weimin Ci

  8. Department of Urology, Beijing Tongren Hospital, Capital Medical University, No. 1 Dongjiaomingxiang Street, Dongcheng District, Beijing, 100730, China

    Kaifang Ma

Authors
  1. Lei Li
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Corresponding authors

Correspondence to Weimin Ci or Kan Gong.

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Funding

This work was supported by the National High-Level Hospital Clinical Research Funding (High-Quality Clinical Research Project of Peking University First Hospital, 2022CR75), National Natural Science Foundation of China (no. 82141103; 82172617; 82172665; 81872081), Scientific Research Seed Fund of Peking University First Hospital (2021SF01; 2023SF40), Capital’s Funds for Health Improvement and Research (2022-2-4074), and Sino-Russian Mathematics Center.

Data availability

The data that support the findings of this study are available in the Genome Sequence Archive for Human (GSA-Human) (https://ngdc.cncb.ac.cn/gsa-human/).

Conflict of interest

The authors Lei Li, Hainan Bao, Yawei Xu, Wuping Yang, Zedan Zhang, Kaifang Ma, Kenan Zhang, Jingcheng Zhou, Yanqing Gong, Weimin Ci, and Kan Gong declare that they have no conflicts of interest that might be relevant to the contents of this manuscript.

Ethical approval

Approval for the study was granted by the ethics committee of Peking University First Hospital, with the assigned number IRB00001052-18004. The study was performed in accordance with the ethical standards as laid down in the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards.

Consent (participation and publication)

Verbal informed consent was obtained from the patients for their anonymized information to be published in this article.

Author contributions

K.G. and W.M.C. were responsible for the overall planning of the study. L.L., H.N.B., and Y.W.X. mainly directed bioinformatics analysis and wrote the paper. W.P.Y., Z.D.Z., and K.F.M. were mainly responsible for the compilation of experimental data. K.N.Z. collected and preserved the samples. J.C.Z. and Y.Q.G. mainly polished the article. All authors contributed critical review of the manuscript, revisions, and have approved its submission.

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Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file 1 Supplementary Table 1. Summary of data generated by genome-wide bisulfite sequencing (XLSX 19 KB)

Supplementary file 2 Supplementary Table 2. Differential methylation area information (XLSX 12244 KB)

Supplementary file 3 Supplementary Table 3. Tumor versus Normal_hypermethylation_anno (XLSX 967 KB)

Supplementary file 4 Supplementary Table 4. Tumor versus Normal_hypomethylation_anno (XLSX 13132 KB)

40291_2023_663_MOESM5_ESM.xlsx

Supplementary file 5 Supplementary Table 5-1. Tumor versus Normal_DMR_up_promoter_metascape_annotation. Supplementary Table 5-2. Tumor versus Normal_DMR_up_promoter_metascape_enrichment (XLSX 234 KB)

40291_2023_663_MOESM6_ESM.xlsx

Supplementary file 6 Supplementary Table 6-1. Tumor versus Normal_DMR_down_promoter_metascape_annotation. Supplementary Table 6-2. Tumor versus Normal_DMR_down_promoter_metascape_enrichment (XLSX 508 KB)

Supplementary file 7 Supplementary Table 7. RNA-seq_DEGs (XLSX 242 KB)

Supplementary file 8 Supplementary Table 8. Tumor versus Normal_hypermethylation and low expression (XLSX 78 KB)

Supplementary file 9 Supplementary Table 9. Tumor versus Normal_hypomethylation and high expression (XLSX 143 KB)

Supplementary file 10 Supplementary Table 10. Hereditary versus Sporadic_DMR (XLSX 564 KB)

Supplementary file11 Supplementary Table 11. Hereditary versus Sporadic_DMR_annotation (XLSX 573 KB)

Supplementary file 12 (DOCX 910 KB)

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Li, L., Bao, H., Xu, Y. et al. Preliminary Study of Whole-Genome Bisulfite Sequencing and Transcriptome Sequencing in VHL Disease-Associated ccRCC. Mol Diagn Ther 27, 741–752 (2023). https://doi.org/10.1007/s40291-023-00663-0

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